Bottom Line:
The PNG haplotypes form a distinct group of clusters not found in any other geographic region.Vaccine haplotypes were rare and geographically restricted, suggesting potentially poor efficacy of candidate PvAMA1 vaccines.It may be possible to cover the existing global PvAMA1 diversity by selection of diverse alleles based on these analyses however it will be important to first define the relationships between the genetic and antigenic diversity of this molecule.

Background: The Plasmodium vivax Apical Membrane Antigen 1 (PvAMA1) is a promising malaria vaccine candidate, however it remains unclear which regions are naturally targeted by host immunity and whether its high genetic diversity will preclude coverage by a monovalent vaccine. To assess its feasibility as a vaccine candidate, we investigated the global population structure of PvAMA1.

Methodology and principal findings: New sequences from Papua New Guinea (PNG, n = 102) were analysed together with published sequences from Thailand (n = 158), India (n = 8), Sri Lanka (n = 23), Venezuela (n = 74) and a collection of isolates from disparate geographic locations (n = 8). A total of 92 single nucleotide polymorphisms (SNPs) were identified including 22 synonymous SNPs and 70 non-synonymous (NS) SNPs. Polymorphisms and signatures of balancing (positive Tajima's D and low FST values) selection were predominantly clustered in domain I, suggesting it is a dominant target of protective immune responses. To estimate global antigenic diversity, haplotypes comprised of (i) non-singleton (n = 40) and (ii) common (≥10% minor allele frequency, n = 23) polymorphic amino acid sites were then analysed revealing a total of 219 and 210 distinct haplotypes, respectively. Although highly diverse, the 210 haplotypes comprised of only common polymorphisms were grouped into eleven clusters, however substantial geographic differentiation was observed, and this may have implications for the efficacy of PvAMA1 vaccines in different malaria-endemic areas. The PNG haplotypes form a distinct group of clusters not found in any other geographic region. Vaccine haplotypes were rare and geographically restricted, suggesting potentially poor efficacy of candidate PvAMA1 vaccines.

Conclusions: It may be possible to cover the existing global PvAMA1 diversity by selection of diverse alleles based on these analyses however it will be important to first define the relationships between the genetic and antigenic diversity of this molecule.

pntd-0002506-g003: Location of 22 polymorphic PvAMA1 residues predicted to be under balancing selection.A) Ribbon diagram of the PvAMA1 model showing each of the PvAMA1 domains (DI in cyan, DII in magenta, and DIII in orange) and the hydrophobic ligand binding cleft (dark blue). Each of the 22 residues under selection and the 12 hydrophobic cleft residues are shown by CPK-models of their atoms (spheres) and are coloured according to location. B) Solvent-accessible surface representation of the ‘active face’ of the PvAMA1 model. The hydrophobic cleft and polymorphic residues are shown, with colouring as described for panel A. C) Solvent-accessible surface representation of the ‘silent face’ of the PvAMA1 model. The hydrophobic cleft and polymorphic residues are shown, with colouring as described for panel A.

Mentions:
All 22 polymorphic residues mapped to solvent-exposed surfaces of the PvAMA1 molecule (Figure 3). Extreme bias in the distribution of polymorphisms was observed, with 21 of the 22 polymorphic residues located on one face of the PvAMA1 structure (Figure 3B). Only the signal sequence polymorphic residue (Arg66) was located on the opposing face (Figure 3C). Four polymorphic residues (Lys120, Asn130, Asn132 and Glu145) were located proximal to the hydrophobic binding cleft in DI loops (Figure 4), three of which aligned with highly polymorphic PfAMA1 residues associated with antigenic escape [38]. The PvAMA1 Lys120 residue aligned with PfAMA1 Tyr175 located within the c3 cluster; PvAMA1 Asn132 and Glu145 aligned with PfAMA1 Glu187 and His200, respectively, located within the c1 cluster (Figure 4, Figure S2).

pntd-0002506-g003: Location of 22 polymorphic PvAMA1 residues predicted to be under balancing selection.A) Ribbon diagram of the PvAMA1 model showing each of the PvAMA1 domains (DI in cyan, DII in magenta, and DIII in orange) and the hydrophobic ligand binding cleft (dark blue). Each of the 22 residues under selection and the 12 hydrophobic cleft residues are shown by CPK-models of their atoms (spheres) and are coloured according to location. B) Solvent-accessible surface representation of the ‘active face’ of the PvAMA1 model. The hydrophobic cleft and polymorphic residues are shown, with colouring as described for panel A. C) Solvent-accessible surface representation of the ‘silent face’ of the PvAMA1 model. The hydrophobic cleft and polymorphic residues are shown, with colouring as described for panel A.

Mentions:
All 22 polymorphic residues mapped to solvent-exposed surfaces of the PvAMA1 molecule (Figure 3). Extreme bias in the distribution of polymorphisms was observed, with 21 of the 22 polymorphic residues located on one face of the PvAMA1 structure (Figure 3B). Only the signal sequence polymorphic residue (Arg66) was located on the opposing face (Figure 3C). Four polymorphic residues (Lys120, Asn130, Asn132 and Glu145) were located proximal to the hydrophobic binding cleft in DI loops (Figure 4), three of which aligned with highly polymorphic PfAMA1 residues associated with antigenic escape [38]. The PvAMA1 Lys120 residue aligned with PfAMA1 Tyr175 located within the c3 cluster; PvAMA1 Asn132 and Glu145 aligned with PfAMA1 Glu187 and His200, respectively, located within the c1 cluster (Figure 4, Figure S2).

Bottom Line:
The PNG haplotypes form a distinct group of clusters not found in any other geographic region.Vaccine haplotypes were rare and geographically restricted, suggesting potentially poor efficacy of candidate PvAMA1 vaccines.It may be possible to cover the existing global PvAMA1 diversity by selection of diverse alleles based on these analyses however it will be important to first define the relationships between the genetic and antigenic diversity of this molecule.

Background: The Plasmodium vivax Apical Membrane Antigen 1 (PvAMA1) is a promising malaria vaccine candidate, however it remains unclear which regions are naturally targeted by host immunity and whether its high genetic diversity will preclude coverage by a monovalent vaccine. To assess its feasibility as a vaccine candidate, we investigated the global population structure of PvAMA1.

Methodology and principal findings: New sequences from Papua New Guinea (PNG, n = 102) were analysed together with published sequences from Thailand (n = 158), India (n = 8), Sri Lanka (n = 23), Venezuela (n = 74) and a collection of isolates from disparate geographic locations (n = 8). A total of 92 single nucleotide polymorphisms (SNPs) were identified including 22 synonymous SNPs and 70 non-synonymous (NS) SNPs. Polymorphisms and signatures of balancing (positive Tajima's D and low FST values) selection were predominantly clustered in domain I, suggesting it is a dominant target of protective immune responses. To estimate global antigenic diversity, haplotypes comprised of (i) non-singleton (n = 40) and (ii) common (≥10% minor allele frequency, n = 23) polymorphic amino acid sites were then analysed revealing a total of 219 and 210 distinct haplotypes, respectively. Although highly diverse, the 210 haplotypes comprised of only common polymorphisms were grouped into eleven clusters, however substantial geographic differentiation was observed, and this may have implications for the efficacy of PvAMA1 vaccines in different malaria-endemic areas. The PNG haplotypes form a distinct group of clusters not found in any other geographic region. Vaccine haplotypes were rare and geographically restricted, suggesting potentially poor efficacy of candidate PvAMA1 vaccines.

Conclusions: It may be possible to cover the existing global PvAMA1 diversity by selection of diverse alleles based on these analyses however it will be important to first define the relationships between the genetic and antigenic diversity of this molecule.